The commandment is "Thou shalt not commit murder" NOT "Thou shalt not kill." There's a huge difference in those things.
That said, I tend to waver a lot on the death penalty and its applications. There is certainly a strong case for it - and a strong case against it. To kill a person is to take away everything they are, and everything they might be from the world. That is a very bad thing. But some crimes are so horrible, and involve such death and the destruction of innocents that the death penalty seems like a not unreasonable recourse.
Sometimes it seems fitting, other times I believe nothing can justify it...
I can never decide.